Ejemplo n.º 1
0
/* 
 * compare to GForward() scores.
 */
static void
utest_fwdback(ESL_RANDOMNESS *r, ESL_ALPHABET *abc, P7_BG *bg, int M, int L, int N)
{
  char        *msg = "forward/backward unit test failed";
  P7_HMM      *hmm = NULL;
  P7_PROFILE  *gm  = NULL;
  P7_OPROFILE *om  = NULL;
  ESL_DSQ     *dsq = malloc(sizeof(ESL_DSQ) * (L+2));
  P7_OMX      *fwd = p7_omx_Create(M, 0, L);
  P7_OMX      *bck = p7_omx_Create(M, 0, L);
  P7_OMX      *oxf = p7_omx_Create(M, L, L);
  P7_OMX      *oxb = p7_omx_Create(M, L, L);
  P7_GMX      *gx  = p7_gmx_Create(M, L);
  float tolerance;
  float fsc1, fsc2;
  float bsc1, bsc2;
  float generic_sc;

  p7_FLogsumInit();
  if (p7_FLogsumError(-0.4, -0.5) > 0.0001) tolerance = 1.0;  /* weaker test against GForward()   */
  else tolerance = 0.0001;   /* stronger test: FLogsum() is in slow exact mode. */

  p7_oprofile_Sample(r, abc, bg, M, L, &hmm, &gm, &om);
  while (N--)
    {
      esl_rsq_xfIID(r, bg->f, abc->K, L, dsq);

      p7_Forward       (dsq, L, om, oxf,      &fsc1);
      p7_Backward      (dsq, L, om, oxf, oxb, &bsc1);
      p7_ForwardParser (dsq, L, om, fwd,      &fsc2);
      p7_BackwardParser(dsq, L, om, fwd, bck, &bsc2);
      p7_GForward      (dsq, L, gm, gx,  &generic_sc);

      /* Forward and Backward scores should agree with high tolerance */
      if (fabs(fsc1-bsc1) > 0.0001)    esl_fatal(msg);
      if (fabs(fsc2-bsc2) > 0.0001)    esl_fatal(msg);
      if (fabs(fsc1-fsc2) > 0.0001)    esl_fatal(msg);

      /* GForward scores should approximate Forward scores, 
       * with tolerance that depends on how logsum.c was compiled
       */
      if (fabs(fsc1-generic_sc) > tolerance) esl_fatal(msg);
    }

  free(dsq);
  p7_hmm_Destroy(hmm);
  p7_omx_Destroy(oxb);
  p7_omx_Destroy(oxf);
  p7_omx_Destroy(bck);
  p7_omx_Destroy(fwd);
  p7_gmx_Destroy(gx);
  p7_profile_Destroy(gm);
  p7_oprofile_Destroy(om);
}
Ejemplo n.º 2
0
/* compare results to GDecoding(). */
static void
utest_null2_expectation(ESL_RANDOMNESS *r, ESL_ALPHABET *abc, P7_BG *bg, int M, int L, int N, float tolerance)
{
  char        *msg  = "decoding unit test failed";
  P7_HMM      *hmm  = NULL;
  P7_PROFILE  *gm   = NULL;
  P7_OPROFILE *om   = NULL;
  ESL_DSQ     *dsq  = malloc(sizeof(ESL_DSQ) * (L+2));
  P7_OMX      *fwd  = p7_omx_Create(M, L, L);
  P7_OMX      *bck  = p7_omx_Create(M, L, L);
  P7_OMX      *pp   = p7_omx_Create(M, L, L);
  P7_GMX      *gxf  = p7_gmx_Create(M, L);
  P7_GMX      *gxb  = p7_gmx_Create(M, L);
  P7_GMX      *gpp  = p7_gmx_Create(M, L);
  float       *on2  = malloc(sizeof(float) * abc->Kp);
  float       *gn2  = malloc(sizeof(float) * abc->Kp);
  float fsc1, fsc2;
  float bsc1, bsc2;

  if (!gn2 || !on2) esl_fatal(msg);

  if (p7_oprofile_Sample(r, abc, bg, M, L, &hmm, &gm, &om) != eslOK) esl_fatal(msg);
  while (N--)
    {
      if (esl_rsq_xfIID(r, bg->f, abc->K, L, dsq) != eslOK) esl_fatal(msg);
      if (p7_Forward       (dsq, L, om, fwd,      &fsc1) != eslOK) esl_fatal(msg);
      if (p7_Backward      (dsq, L, om, fwd, bck, &bsc1) != eslOK) esl_fatal(msg);
      if (p7_Decoding(om, fwd, bck, pp)                  != eslOK) esl_fatal(msg);
      if (p7_Null2_ByExpectation(om, pp, on2)            != eslOK) esl_fatal(msg);
      
      if (p7_GForward (dsq, L, gm, gxf, &fsc2)           != eslOK) esl_fatal(msg);
      if (p7_GBackward(dsq, L, gm, gxb, &bsc2)           != eslOK) esl_fatal(msg);
      if (p7_GDecoding(gm, gxf, gxb, gpp)                != eslOK) esl_fatal(msg);
      if (p7_GNull2_ByExpectation(gm, gpp, gn2)          != eslOK) esl_fatal(msg);

      if (esl_vec_FCompare(gn2, on2, abc->Kp, tolerance) != eslOK) esl_fatal(msg);
    }

  p7_gmx_Destroy(gpp);
  p7_gmx_Destroy(gxf);
  p7_gmx_Destroy(gxb);
  p7_omx_Destroy(pp);
  p7_omx_Destroy(fwd);
  p7_omx_Destroy(bck);
  free(on2);
  free(gn2);
  free(dsq);
  p7_oprofile_Destroy(om);
  p7_profile_Destroy(gm);
  p7_hmm_Destroy(hmm);
}
Ejemplo n.º 3
0
/* compare results to GDecoding(). */
static void
utest_decoding(ESL_RANDOMNESS *r, ESL_ALPHABET *abc, P7_BG *bg, int M, int L, int N, float tolerance)
{
  char        *msg  = "decoding unit test failed";
  P7_HMM      *hmm  = NULL;
  P7_PROFILE  *gm   = NULL;
  P7_OPROFILE *om   = NULL;
  ESL_DSQ     *dsq  = malloc(sizeof(ESL_DSQ) * (L+2));
  P7_OMX      *fwd  = p7_omx_Create(M, L, L);
  P7_OMX      *bck  = p7_omx_Create(M, L, L);
  P7_OMX      *pp   = p7_omx_Create(M, L, L);
  P7_GMX      *gxf  = p7_gmx_Create(M, L);
  P7_GMX      *gxb  = p7_gmx_Create(M, L);
  P7_GMX      *gxp1 = p7_gmx_Create(M, L);
  P7_GMX      *gxp2 = p7_gmx_Create(M, L);
  float fsc1, fsc2;
  float bsc1, bsc2;

  if (p7_oprofile_Sample(r, abc, bg, M, L, &hmm, &gm, &om) != eslOK) esl_fatal(msg);
  while (N--)
    {
      if (esl_rsq_xfIID(r, bg->f, abc->K, L, dsq) != eslOK) esl_fatal(msg);
      if (p7_Forward       (dsq, L, om, fwd,      &fsc1) != eslOK) esl_fatal(msg);
      if (p7_Backward      (dsq, L, om, fwd, bck, &bsc1) != eslOK) esl_fatal(msg);
      if (p7_Decoding(om, fwd, bck, pp)                  != eslOK) esl_fatal(msg);
      if (p7_omx_FDeconvert(pp, gxp1)                    != eslOK) esl_fatal(msg);
      
      if (p7_GForward (dsq, L, gm, gxf, &fsc2)           != eslOK) esl_fatal(msg);
      if (p7_GBackward(dsq, L, gm, gxb, &bsc2)           != eslOK) esl_fatal(msg);
      if (p7_GDecoding(gm, gxf, gxb, gxp2)               != eslOK) esl_fatal(msg);

      // p7_gmx_Dump(stdout, gxp1, p7_DEFAULT);
      // p7_gmx_Dump(stdout, gxp2, p7_DEFAULT);

      if (p7_gmx_Compare(gxp1, gxp2, tolerance)          != eslOK) esl_fatal(msg);
    }

  p7_gmx_Destroy(gxp1);
  p7_gmx_Destroy(gxp2);
  p7_gmx_Destroy(gxf);
  p7_gmx_Destroy(gxb);
  p7_omx_Destroy(fwd);
  p7_omx_Destroy(bck);
  p7_omx_Destroy(pp);
  free(dsq);
  p7_oprofile_Destroy(om);
  p7_profile_Destroy(gm);
  p7_hmm_Destroy(hmm);
}
Ejemplo n.º 4
0
/* Function:  p7_ViterbiMu()
 * Synopsis:  Determines the local Viterbi Gumbel mu parameter for a model.
 * Incept:    SRE, Tue May 19 10:26:19 2009 [Janelia]
 *
 * Purpose:   Identical to p7_MSVMu(), above, except that it fits
 *            Viterbi scores instead of MSV scores. 
 *
 *            The difference between the two mus is small, but can be
 *            up to ~1 bit or so for large, low-info models [J4/126] so
 *            decided to calibrate the two mus separately [J5/8]. 
 *            
 * Args:      r       :  source of random numbers
 *            om      :  score profile (length config is changed upon return!)
 *            bg      :  null model    (length config is changed upon return!)
 *            L       :  length of sequences to simulate
 *            N	      :  number of sequences to simulate		
 *            lambda  :  known Gumbel lambda parameter
 *            ret_vmu :  RETURN: ML estimate of location param mu
 *
 * Returns:   <eslOK> on success, and <ret_mu> contains the ML estimate
 *            of $\mu$.
 *
 * Throws:    (no abnormal error conditions)
 */
int
p7_ViterbiMu(ESL_RANDOMNESS *r, P7_OPROFILE *om, P7_BG *bg, int L, int N, double lambda, double *ret_vmu)
{
  P7_OMX  *ox      = p7_omx_Create(om->M, 0, 0); /* DP matrix: 1 row version */
  ESL_DSQ *dsq     = NULL;
  double  *xv      = NULL;
  int      i;
  float    sc, nullsc;
#ifndef p7_IMPL_DUMMY
  float    maxsc   = (32767.0 - om->base_w) / om->scale_w; /* if score overflows, use this [J4/139] */
#endif
  int      status;

  if (ox == NULL) { status = eslEMEM; goto ERROR; }
  ESL_ALLOC(xv,  sizeof(double)  * N);
  ESL_ALLOC(dsq, sizeof(ESL_DSQ) * (L+2));

  p7_oprofile_ReconfigLength(om, L);
  p7_bg_SetLength(bg, L);

  for (i = 0; i < N; i++)
    {
      if ((status = esl_rsq_xfIID(r, bg->f, om->abc->K, L, dsq)) != eslOK) goto ERROR;
      if ((status = p7_bg_NullOne(bg, dsq, L, &nullsc))          != eslOK) goto ERROR;   

      status = p7_ViterbiFilter(dsq, L, om, ox, &sc); 
#ifndef p7_IMPL_DUMMY
      if (status == eslERANGE) { sc = maxsc; status = eslOK; }
#endif
      if (status != eslOK)     goto ERROR;

      xv[i] = (sc - nullsc) / eslCONST_LOG2;
    }

  if ((status = esl_gumbel_FitCompleteLoc(xv, N, lambda, ret_vmu))  != eslOK) goto ERROR;
  p7_omx_Destroy(ox);
  free(xv);
  free(dsq);
  return eslOK;

 ERROR:
  *ret_vmu = 0.0;
  if (ox  != NULL) p7_omx_Destroy(ox);
  if (xv  != NULL) free(xv);
  if (dsq != NULL) free(dsq);
  return status;

}
Ejemplo n.º 5
0
/* ViterbiScore() unit test
 * 
 * We can compare these scores to GViterbi() almost exactly; the only
 * differences should be negligible roundoff errors. Must convert
 * the optimized profile to lspace, though, rather than pspace.
 */
static void
utest_viterbi_score(ESL_RANDOMNESS *r, ESL_ALPHABET *abc, P7_BG *bg, int M, int L, int N)
{
  P7_HMM      *hmm = NULL;
  P7_PROFILE  *gm  = NULL;
  P7_OPROFILE *om  = NULL;
  ESL_DSQ     *dsq = malloc(sizeof(ESL_DSQ) * (L+2));
  P7_OMX      *ox  = p7_omx_Create(M, 0, 0);
  P7_GMX      *gx  = p7_gmx_Create(M, L);
  float sc1, sc2;

  p7_oprofile_Sample(r, abc, bg, M, L, &hmm, &gm, &om);
  p7_oprofile_Logify(om);
  while (N--)
    {
      esl_rsq_xfIID(r, bg->f, abc->K, L, dsq);

      p7_ViterbiScore(dsq, L, om, ox, &sc1);
      p7_GViterbi    (dsq, L, gm, gx, &sc2);

      if (fabs(sc1-sc2) > 0.001) esl_fatal("viterbi score unit test failed: scores differ");
    }

  free(dsq);
  p7_hmm_Destroy(hmm);
  p7_omx_Destroy(ox);
  p7_gmx_Destroy(gx);
  p7_profile_Destroy(gm);
  p7_oprofile_Destroy(om);
}
Ejemplo n.º 6
0
/* tests: 
 *   1. each sampled trace must validate.
 *   2. each trace must be <= viterbi trace score
 *   3. in a large # of traces, one is "equal" to the viterbi trace score.
 *      (this of course is stochastic; but it's true for the particular
 *       choice of RNG seed used in tests here.)
 */
static void
utest_stotrace(ESL_GETOPTS *go, ESL_RANDOMNESS *rng, ESL_ALPHABET *abc, P7_PROFILE *gm, P7_OPROFILE *om, ESL_DSQ *dsq, int L, int ntrace)
{
  P7_GMX   *gx  = NULL;
  P7_OMX   *ox  = NULL;
  P7_TRACE *tr  = NULL;
  char      errbuf[eslERRBUFSIZE];
  int       idx;
  float     maxsc = -eslINFINITY;
  float     vsc, sc;

  if ((gx     = p7_gmx_Create(gm->M, L))        == NULL)  esl_fatal("generic DP matrix creation failed");
  if ((ox     = p7_omx_Create(gm->M, L, L))     == NULL)  esl_fatal("optimized DP matrix create failed");
  if ((tr     = p7_trace_Create())              == NULL)  esl_fatal("trace creation failed");

  if (p7_GViterbi(dsq, L, gm, gx, &vsc)         != eslOK) esl_fatal("viterbi failed");
  if (p7_Forward (dsq, L, om, ox, NULL)         != eslOK) esl_fatal("forward failed");

  for (idx = 0; idx < ntrace; idx++)
    {
      if (p7_StochasticTrace(rng, dsq, L, om, ox, tr) != eslOK) esl_fatal("stochastic trace failed");
      if (p7_trace_Validate(tr, abc, dsq, errbuf)     != eslOK) esl_fatal("trace invalid:\n%s", errbuf);
      if (p7_trace_Score(tr, dsq, gm, &sc)            != eslOK) esl_fatal("trace scoring failed"); 

      maxsc = ESL_MAX(sc, maxsc);
      if (sc > vsc) esl_fatal("sampled trace has score > optimal Viterbi path; not possible");
      p7_trace_Reuse(tr);
    }
  if (esl_FCompare(maxsc, vsc, 0.1) != eslOK) esl_fatal("stochastic trace failed to sample the Viterbi path");
  
  p7_trace_Destroy(tr);
  p7_omx_Destroy(ox);
  p7_gmx_Destroy(gx);
}
Ejemplo n.º 7
0
void destroy_hmmer_wrapper() {
  int index;
  if(models != NULL) {
    for(index = 0;index < num_models;index++) {
      p7_oprofile_Destroy(models[index]);
      p7_profile_Destroy(gmodels[index]);
    }
    free(models);
    free(gmodels);
  }

  if(wrapper_results != NULL) {
    for(index = 0;index < num_models;index++) {
      destroy_result(wrapper_results[index]);
    }
    free(wrapper_results);
  }
  
  if(bg != NULL) {
    p7_bg_Destroy(bg);
  }

  if(hmm_fp != NULL) {
    p7_hmmfile_Close(hmm_fp);
  }

  if(oxf) {
    p7_omx_Destroy(oxf);
  }
  if(oxb) {
    p7_omx_Destroy(oxb);
  }

  if(gxf) {
    p7_gmx_Destroy(gxf);
  }
  if(gxb) {
    p7_gmx_Destroy(gxb);
  }

  if(abc) {
    esl_alphabet_Destroy(abc);
  }
  if(tr) {
    p7_trace_Destroy(tr);
  }
}
Ejemplo n.º 8
0
/* Function:  p7_Tau()
 * Synopsis:  Determine Forward tau by brief simulation.
 * Incept:    SRE, Thu Aug  9 15:08:39 2007 [Janelia]
 *
 * Purpose:   Determine the <tau> parameter for an exponential tail fit
 *            to the Forward score distribution for model <om>, on
 *            random sequences with the composition of the background
 *            model <bg>. This <tau> parameter is for an exponential
 *            distribution anchored from $P=1.0$, so it's not really a
 *            tail per se; but it's only an accurate fit in the tail
 *            of the Forward score distribution, from about $P=0.001$
 *            or so.
 *            
 *            The determination of <tau> is done by a brief simulation
 *            in which we fit a Gumbel distribution to a small number
 *            of Forward scores of random sequences, and use that to
 *            predict the location of the tail at probability <tailp>.
 *            
 *            The Gumbel is of course inaccurate, but we can use it
 *            here solely as an empirical distribution to determine
 *            the location of a reasonable <tau> more accurately on a
 *            smaller number of samples than we could do with raw
 *            order statistics. 
 *            
 *            Typical choices are L=100, N=200, tailp=0.04, which
 *            typically yield estimates $\hat{\mu}$ with a precision
 *            (standard deviation) of $\pm$ 0.2 bits, corresponding to
 *            a $\pm$ 15\% error in E-values. See [J1/135].
 *            
 *            The use of Gumbel fitting to a small number of $N$
 *            samples and the extrapolation of $\hat{\mu}$ from the
 *            estimated location of the 0.04 tail mass are both
 *            empirical and carefully optimized against several
 *            tradeoffs. Most importantly, around this choice of tail
 *            probability, a systematic error introduced by the use of
 *            the Gumbel fit is being cancelled by systematic error
 *            introduced by the use of a higher tail probability than
 *            the regime in which the exponential tail is a valid
 *            approximation. See [J1/135] for discussion.
 *            
 *            This function changes the length configuration of both
 *            <om> and <bg>. The caller must remember to reconfigure
 *            both of their length models appropriately for any
 *            subsequent alignments.
 *            
 * Args:      r      : source of randomness
 *            om     : configured profile to sample sequences from
 *            bg     : null model (for background residue frequencies)
 *            L      : mean length model for seq emission from profile
 *            N      : number of sequences to generate
 *            lambda : expected slope of the exponential tail (from p7_Lambda())
 *            tailp  : tail mass from which we will extrapolate mu
 *            ret_mu : RETURN: estimate for the Forward mu (base of exponential tail)
 *
 * Returns:   <eslOK> on success, and <*ret_fv> is the score difference
 *            in bits.
 *
 * Throws:    <eslEMEM> on allocation error, and <*ret_fv> is 0.
 */
int
p7_Tau(ESL_RANDOMNESS *r, P7_OPROFILE *om, P7_BG *bg, int L, int N, double lambda, double tailp, double *ret_tau)
{
  P7_OMX  *ox      = p7_omx_Create(om->M, 0, L);     /* DP matrix: for ForwardParser,  L rows */
  ESL_DSQ *dsq     = NULL;
  double  *xv      = NULL;
  float    fsc, nullsc;		                  
  double   gmu, glam;
  int      status;
  int      i;

  ESL_ALLOC(xv,  sizeof(double)  * N);
  ESL_ALLOC(dsq, sizeof(ESL_DSQ) * (L+2));
  if (ox == NULL) { status = eslEMEM; goto ERROR; }

  p7_oprofile_ReconfigLength(om, L);
  p7_bg_SetLength(bg, L);

  for (i = 0; i < N; i++)
    {
      if ((status = esl_rsq_xfIID(r, bg->f, om->abc->K, L, dsq)) != eslOK) goto ERROR;
      if ((status = p7_ForwardParser(dsq, L, om, ox, &fsc))      != eslOK) goto ERROR;
      if ((status = p7_bg_NullOne(bg, dsq, L, &nullsc))          != eslOK) goto ERROR;   
      xv[i] = (fsc - nullsc) / eslCONST_LOG2;
    }
  if ((status = esl_gumbel_FitComplete(xv, N, &gmu, &glam)) != eslOK) goto ERROR;

  /* Explanation of the eqn below: first find the x at which the Gumbel tail
   * mass is predicted to be equal to tailp. Then back up from that x
   * by log(tailp)/lambda to set the origin of the exponential tail to 1.0
   * instead of tailp.
   */
  *ret_tau =  esl_gumbel_invcdf(1.0-tailp, gmu, glam) + (log(tailp) / lambda);
  
  free(xv);
  free(dsq);
  p7_omx_Destroy(ox);
  return eslOK;

 ERROR:
  *ret_tau = 0.;
  if (xv  != NULL) free(xv);
  if (dsq != NULL) free(dsq);
  if (ox  != NULL) p7_omx_Destroy(ox);
  return status;
}
Ejemplo n.º 9
0
/* Function:  p7_omx_Create()
 * Synopsis:  Create an optimized dynamic programming matrix.
 * Incept:    SRE, Tue Nov 27 08:48:20 2007 [Janelia]
 *
 * Purpose:   Allocates a reusable, resizeable <P7_OMX> for models up to
 *            size <allocM> and target sequences up to length
 *            <allocL/allocXL>, for use by any of the various optimized
 *            DP routines.
 *            
 *            To allocate the very memory-efficient one-row matrix
 *            used by *Filter() and *Score() functions that only
 *            calculate scores, <allocM=M>, <allocL=0>, and
 *            <allocXL=0>.
 *            
 *            To allocate the reasonably memory-efficient linear
 *            arrays used by *Parser() functions that only keep
 *            special (X) state scores, <allocM=M>, <allocL=0>,
 *            and <allocXL=L>.
 *            
 *            To allocate a complete matrix suitable for functions
 *            that need the whole DP matrix for traceback, sampling,
 *            posterior decoding, or reestimation, <allocM=M> and
 *            <allocL=allocXL=L>.
 *
 * Returns:   a pointer to the new <P7_OMX>.
 *
 * Throws:    <NULL> on allocation failure.
 */
P7_OMX *
p7_omx_Create(int allocM, int allocL, int allocXL)
{
  P7_OMX  *ox     = NULL;
  int      i;
  int      status;

  ESL_ALLOC(ox, sizeof(P7_OMX));
  ox->dp_mem = NULL;
  ox->dpb    = NULL;
  ox->dpw    = NULL;
  ox->dpf    = NULL;
  ox->xmx    = NULL;
  ox->x_mem  = NULL;

  /* DP matrix will be allocated for allocL+1 rows 0,1..L; allocQ4*p7X_NSCELLS columns */
  ox->allocR   = allocL+1;
  ox->validR   = ox->allocR;
  ox->allocQ4  = p7O_NQF(allocM);
  ox->allocQ8  = p7O_NQW(allocM);
  ox->allocQ16 = p7O_NQB(allocM);
  ox->ncells   = ox->allocR * ox->allocQ4 * 4;      /* # of DP cells allocated, where 1 cell contains MDI */

  /* floats always dominate; +15 for alignment */
  ESL_ALLOC(ox->dp_mem, sizeof(vector float) * ox->allocR * ox->allocQ4 * p7X_NSCELLS + 15);
  ESL_ALLOC(ox->dpb,    sizeof(vector unsigned char *) * ox->allocR);
  ESL_ALLOC(ox->dpw,    sizeof(vector signed short *)  * ox->allocR);
  ESL_ALLOC(ox->dpf,    sizeof(vector float *)         * ox->allocR);

  /* DP memory shared by <dpb>, <dpw>, <dpf> */
  ox->dpb[0] = (vector unsigned char *) ((unsigned long int) ((char *) ox->dp_mem + 15) & (~0xf));
  ox->dpw[0] = (vector signed short *)  ox->dpb[0];
  ox->dpf[0] = (vector float *)         ox->dpb[0];

  for (i = 1; i <= allocL; i++) {
    ox->dpf[i] = ox->dpf[0] + i * ox->allocQ4  * p7X_NSCELLS;
    ox->dpw[i] = ox->dpw[0] + i * ox->allocQ8  * p7X_NSCELLS;
    ox->dpb[i] = ox->dpb[0] + i * ox->allocQ16;
  }

  ox->allocXR = allocXL+1;
  ESL_ALLOC(ox->x_mem,  sizeof(float) * ox->allocXR * p7X_NXCELLS + 15); 
  ox->xmx = (float *) ((unsigned long int) ((char *) ox->x_mem  + 15) & (~0xf));

  ox->M              = 0;
  ox->L              = 0;
  ox->totscale       = 0.0;
  ox->has_own_scales = TRUE;	/* most matrices are Forward, control their own scale factors */
#ifdef p7_DEBUGGING
  ox->debugging = FALSE;
  ox->dfp       = NULL;
#endif
  return ox;

 ERROR:
  p7_omx_Destroy(ox);
  return NULL;
}
Ejemplo n.º 10
0
/* ViterbiFilter() unit test
 * 
 * We can check that scores are identical (within machine error) to
 * scores of generic DP with scores rounded the same way.  Do this for
 * a random model of length <M>, for <N> test sequences of length <L>.
 * 
 * We assume that we don't accidentally generate a high-scoring random
 * sequence that overflows ViterbiFilter()'s limited range.
 * 
 */
static void
utest_viterbi_filter(ESL_RANDOMNESS *r, ESL_ALPHABET *abc, P7_BG *bg, int M, int L, int N)
{
  P7_HMM      *hmm = NULL;
  P7_PROFILE  *gm  = NULL;
  P7_OPROFILE *om  = NULL;
  ESL_DSQ     *dsq = malloc(sizeof(ESL_DSQ) * (L+2));
  P7_OMX      *ox  = p7_omx_Create(M, 0, 0);
  P7_GMX      *gx  = p7_gmx_Create(M, L);
  float sc1, sc2;

  p7_oprofile_Sample(r, abc, bg, M, L, &hmm, &gm, &om);
  p7_profile_SameAsVF(om, gm);	/* round and scale the scores in <gm> the same as in <om> */

#if 0
  p7_oprofile_Dump(stdout, om);              // dumps the optimized profile
  p7_omx_SetDumpMode(stdout, ox, TRUE);      // makes the fast DP algorithms dump their matrices
#endif

  while (N--)
    {
      esl_rsq_xfIID(r, bg->f, abc->K, L, dsq);

      p7_ViterbiFilter(dsq, L, om, ox, &sc1);
      p7_GViterbi     (dsq, L, gm, gx, &sc2);

#if 0
      p7_gmx_Dump(stdout, gx);              // dumps a generic DP matrix
#endif
      
      sc2 /= om->scale_w;
      sc2 -= 3.0;

      if (fabs(sc1-sc2) > 0.001) esl_fatal("viterbi filter unit test failed: scores differ (%.2f, %.2f)", sc1, sc2);
    }

  free(dsq);
  p7_hmm_Destroy(hmm);
  p7_omx_Destroy(ox);
  p7_gmx_Destroy(gx);
  p7_profile_Destroy(gm);
  p7_oprofile_Destroy(om);
}
Ejemplo n.º 11
0
int 
main(int argc, char **argv)
{
  ESL_GETOPTS    *go      = p7_CreateDefaultApp(options, 1, argc, argv, banner, usage);
  char           *hmmfile = esl_opt_GetArg(go, 1);
  ESL_STOPWATCH  *w       = esl_stopwatch_Create();
  ESL_RANDOMNESS *r       = esl_randomness_CreateFast(esl_opt_GetInteger(go, "-s"));
  ESL_ALPHABET   *abc     = NULL;
  P7_HMMFILE     *hfp     = NULL;
  P7_HMM         *hmm     = NULL;
  P7_BG          *bg      = NULL;
  P7_PROFILE     *gm      = NULL;
  P7_OPROFILE    *om      = NULL;
  P7_GMX         *gx1     = NULL;
  P7_GMX         *gx2     = NULL;
  P7_OMX         *ox1     = NULL;
  P7_OMX         *ox2     = NULL;
  P7_TRACE       *tr      = NULL;
  int             L       = esl_opt_GetInteger(go, "-L");
  int             N       = esl_opt_GetInteger(go, "-N");
  ESL_DSQ        *dsq     = malloc(sizeof(ESL_DSQ) * (L+2));
  int             i;
  float           fsc, bsc, accscore;
  float           fsc_g, bsc_g, accscore_g;
  double          Mcs;

  p7_FLogsumInit();

  if (p7_hmmfile_OpenE(hmmfile, NULL, &hfp, NULL) != eslOK) p7_Fail("Failed to open HMM file %s", hmmfile);
  if (p7_hmmfile_Read(hfp, &abc, &hmm)            != eslOK) p7_Fail("Failed to read HMM");

  bg = p7_bg_Create(abc);                 p7_bg_SetLength(bg, L);
  gm = p7_profile_Create(hmm->M, abc);    p7_ProfileConfig(hmm, bg, gm, L, p7_LOCAL);
  om = p7_oprofile_Create(gm->M, abc);    p7_oprofile_Convert(gm, om);
  p7_oprofile_ReconfigLength(om, L);

  if (esl_opt_GetBoolean(go, "-x") && p7_FLogsumError(-0.4, -0.5) > 0.0001)
    p7_Fail("-x here requires p7_Logsum() recompiled in slow exact mode");

  ox1 = p7_omx_Create(gm->M, L, L);
  ox2 = p7_omx_Create(gm->M, L, L);
  tr  = p7_trace_CreateWithPP();

  esl_rsq_xfIID(r, bg->f, abc->K, L, dsq);
  p7_Forward (dsq, L, om, ox1,      &fsc);
  p7_Backward(dsq, L, om, ox1, ox2, &bsc);
  p7_Decoding(om, ox1, ox2, ox2);              

  esl_stopwatch_Start(w);
  for (i = 0; i < N; i++)
    {
      p7_OptimalAccuracy(om, ox2, ox1, &accscore);

      if (! esl_opt_GetBoolean(go, "--notrace"))
	{
	  p7_OATrace(om, ox2, ox1, tr);
	  p7_trace_Reuse(tr);
	}
    }
  esl_stopwatch_Stop(w);

  Mcs        = (double) N * (double) L * (double) gm->M * 1e-6 / (double) w->user;
  esl_stopwatch_Display(stdout, w, "# CPU time: ");
  printf("# M    = %d\n",   gm->M);
  printf("# %.1f Mc/s\n", Mcs);

  if (esl_opt_GetBoolean(go, "-c") || esl_opt_GetBoolean(go, "-x") )
    {
      gx1 = p7_gmx_Create(gm->M, L);
      gx2 = p7_gmx_Create(gm->M, L);
      
      p7_GForward (dsq, L, gm, gx1, &fsc_g);
      p7_GBackward(dsq, L, gm, gx2, &bsc_g);
      p7_GDecoding(gm, gx1, gx2, gx2);             
      p7_GOptimalAccuracy(gm, gx2, gx1, &accscore_g);

      printf("generic:  fwd=%8.4f  bck=%8.4f  acc=%8.4f\n", fsc_g, bsc_g, accscore_g);
      printf("VMX:      fwd=%8.4f  bck=%8.4f  acc=%8.4f\n", fsc,   bsc,   accscore);

      p7_gmx_Destroy(gx1);
      p7_gmx_Destroy(gx2);
    }

  free(dsq);
  p7_omx_Destroy(ox1);
  p7_omx_Destroy(ox2);
  p7_trace_Destroy(tr);
  p7_oprofile_Destroy(om);
  p7_profile_Destroy(gm);
  p7_bg_Destroy(bg);
  p7_hmm_Destroy(hmm);
  p7_hmmfile_Close(hfp);
  esl_alphabet_Destroy(abc);
  esl_stopwatch_Destroy(w);
  esl_randomness_Destroy(r);
  esl_getopts_Destroy(go);
  return 0;
}
Ejemplo n.º 12
0
int 
main(int argc, char **argv)
{
  ESL_GETOPTS    *go      = esl_getopts_CreateDefaultApp(options, 2, argc, argv, banner, usage);
  char           *hmmfile = esl_opt_GetArg(go, 1);
  char           *seqfile = esl_opt_GetArg(go, 2);
  ESL_ALPHABET   *abc     = NULL;
  P7_HMMFILE     *hfp     = NULL;
  P7_HMM         *hmm     = NULL;
  P7_BG          *bg      = NULL;
  P7_PROFILE     *gm      = NULL;
  P7_OPROFILE    *om      = NULL;
  P7_OMX         *ox      = NULL;
  P7_GMX         *gx      = NULL;
  ESL_SQ         *sq      = NULL;
  ESL_SQFILE     *sqfp    = NULL;
  int             format  = eslSQFILE_UNKNOWN;
  float           vfraw, nullsc, vfscore;
  float           graw, gscore;
  double          P, gP;
  int             status;

  /* Read in one HMM */
  if (p7_hmmfile_Open(hmmfile, NULL, &hfp) != eslOK) p7_Fail("Failed to open HMM file %s", hmmfile);
  if (p7_hmmfile_Read(hfp, &abc, &hmm)     != eslOK) p7_Fail("Failed to read HMM");

  /* Read in one sequence */
  sq     = esl_sq_CreateDigital(abc);
  status = esl_sqfile_Open(seqfile, format, NULL, &sqfp);
  if      (status == eslENOTFOUND) p7_Fail("No such file.");
  else if (status == eslEFORMAT)   p7_Fail("Format unrecognized.");
  else if (status == eslEINVAL)    p7_Fail("Can't autodetect stdin or .gz.");
  else if (status != eslOK)        p7_Fail("Open failed, code %d.", status);

  /* create default null model, then create and optimize profile */
  bg = p7_bg_Create(abc);
  p7_bg_SetLength(bg, sq->n);
  gm = p7_profile_Create(hmm->M, abc);
  p7_ProfileConfig(hmm, bg, gm, sq->n, p7_LOCAL);
  om = p7_oprofile_Create(gm->M, abc);
  p7_oprofile_Convert(gm, om);

  /* allocate DP matrices, both a generic and an optimized one */
  ox = p7_omx_Create(gm->M, 0, sq->n);
  gx = p7_gmx_Create(gm->M, sq->n);

  /* Useful to place and compile in for debugging: 
     p7_oprofile_Dump(stdout, om);      dumps the optimized profile
     p7_omx_SetDumpMode(ox, TRUE);      makes the fast DP algorithms dump their matrices
     p7_gmx_Dump(stdout, gx);           dumps a generic DP matrix
  */

  while ((status = esl_sqio_Read(sqfp, sq)) == eslOK)
    {
      p7_oprofile_ReconfigLength(om, sq->n);
      p7_ReconfigLength(gm,          sq->n);
      p7_bg_SetLength(bg,            sq->n);
      p7_omx_GrowTo(ox, om->M, 0,    sq->n); 
      p7_gmx_GrowTo(gx, gm->M,       sq->n); 

      p7_ViterbiFilter  (sq->dsq, sq->n, om, ox, &vfraw);
      p7_bg_NullOne (bg, sq->dsq, sq->n, &nullsc);
      vfscore = (vfraw - nullsc) / eslCONST_LOG2;
      P        = esl_gumbel_surv(vfscore,  om->evparam[p7_VMU],  om->evparam[p7_VLAMBDA]);

      p7_GViterbi       (sq->dsq, sq->n, gm, gx, &graw); 
      gscore   = (graw - nullsc) / eslCONST_LOG2;
      gP       = esl_gumbel_surv(gscore,  gm->evparam[p7_VMU],  gm->evparam[p7_VLAMBDA]);

      if (esl_opt_GetBoolean(go, "-1"))
	{
	  printf("%-30s\t%-20s\t%9.2g\t%7.2f\t%9.2g\t%7.2f\n", sq->name, hmm->name, P, vfscore, gP, gscore);
	}
      else if (esl_opt_GetBoolean(go, "-P"))
	{ /* output suitable for direct use in profmark benchmark postprocessors: */
	  printf("%g\t%.2f\t%s\t%s\n", P, vfscore, sq->name, hmm->name);
	}
      else
	{
	  printf("target sequence:      %s\n",        sq->name);
	  printf("vit filter raw score: %.2f nats\n", vfraw);
	  printf("null score:           %.2f nats\n", nullsc);
	  printf("per-seq score:        %.2f bits\n", vfscore);
	  printf("P-value:              %g\n",        P);
	  printf("GViterbi raw score:   %.2f nats\n", graw);
	  printf("GViterbi seq score:   %.2f bits\n", gscore);
	  printf("GViterbi P-value:     %g\n",        gP);
	}
      
      esl_sq_Reuse(sq);
    }

  /* cleanup */
  esl_sq_Destroy(sq);
  esl_sqfile_Close(sqfp);
  p7_omx_Destroy(ox);
  p7_gmx_Destroy(gx);
  p7_oprofile_Destroy(om);
  p7_profile_Destroy(gm);
  p7_bg_Destroy(bg);
  p7_hmm_Destroy(hmm);
  p7_hmmfile_Close(hfp);
  esl_alphabet_Destroy(abc);
  esl_getopts_Destroy(go);
  return 0;
}
Ejemplo n.º 13
0
int 
main(int argc, char **argv)
{
  ESL_GETOPTS    *go      = esl_getopts_CreateDefaultApp(options, 1, argc, argv, banner, usage);
  char           *hmmfile = esl_opt_GetArg(go, 1);
  ESL_STOPWATCH  *w       = esl_stopwatch_Create();
  ESL_RANDOMNESS *r       = esl_randomness_CreateFast(esl_opt_GetInteger(go, "-s"));
  ESL_ALPHABET   *abc     = NULL;
  P7_HMMFILE     *hfp     = NULL;
  P7_HMM         *hmm     = NULL;
  P7_BG          *bg      = NULL;
  P7_PROFILE     *gm      = NULL;
  P7_OPROFILE    *om      = NULL;
  P7_OMX         *ox      = NULL;
  P7_GMX         *gx      = NULL;
  int             L       = esl_opt_GetInteger(go, "-L");
  int             N       = esl_opt_GetInteger(go, "-N");
  ESL_DSQ        *dsq     = malloc(sizeof(ESL_DSQ) * (L+2));
  int             i;
  float           sc1, sc2;
  double          base_time, bench_time, Mcs;

  if (p7_hmmfile_Open(hmmfile, NULL, &hfp) != eslOK) p7_Fail("Failed to open HMM file %s", hmmfile);
  if (p7_hmmfile_Read(hfp, &abc, &hmm)     != eslOK) p7_Fail("Failed to read HMM");

  bg = p7_bg_Create(abc);
  p7_bg_SetLength(bg, L);
  gm = p7_profile_Create(hmm->M, abc);
  p7_ProfileConfig(hmm, bg, gm, L, p7_LOCAL);
  om = p7_oprofile_Create(gm->M, abc);
  p7_oprofile_Convert(gm, om);
  p7_oprofile_ReconfigLength(om, L);

  if (esl_opt_GetBoolean(go, "-x")) p7_profile_SameAsVF(om, gm);

  ox = p7_omx_Create(gm->M, 0, 0);
  gx = p7_gmx_Create(gm->M, L);

  /* Get a baseline time: how long it takes just to generate the sequences */
  esl_stopwatch_Start(w);
  for (i = 0; i < N; i++)
    esl_rsq_xfIID(r, bg->f, abc->K, L, dsq);
  esl_stopwatch_Stop(w);
  base_time = w->user;

  /* Run the benchmark */
  esl_stopwatch_Start(w);
  for (i = 0; i < N; i++)
    {
      esl_rsq_xfIID(r, bg->f, abc->K, L, dsq);
      p7_ViterbiFilter(dsq, L, om, ox, &sc1);   

      if (esl_opt_GetBoolean(go, "-c")) 
	{
	  p7_GViterbi(dsq, L, gm, gx, &sc2); 
	  printf("%.4f %.4f\n", sc1, sc2);  
	}

      if (esl_opt_GetBoolean(go, "-x"))
	{
	  p7_GViterbi(dsq, L, gm, gx, &sc2); 
	  sc2 /= om->scale_w;
	  if (om->mode == p7_UNILOCAL)   sc2 -= 2.0; /* that's ~ L \log \frac{L}{L+2}, for our NN,CC,JJ */
	  else if (om->mode == p7_LOCAL) sc2 -= 3.0; /* that's ~ L \log \frac{L}{L+3}, for our NN,CC,JJ */
	  printf("%.4f %.4f\n", sc1, sc2);  
	}
    }
  esl_stopwatch_Stop(w);
  bench_time = w->user - base_time;
  Mcs        = (double) N * (double) L * (double) gm->M * 1e-6 / (double) bench_time;
  esl_stopwatch_Display(stdout, w, "# CPU time: ");
  printf("# M    = %d\n",   gm->M);
  printf("# %.1f Mc/s\n", Mcs);

  free(dsq);
  p7_omx_Destroy(ox);
  p7_gmx_Destroy(gx);
  p7_oprofile_Destroy(om);
  p7_profile_Destroy(gm);
  p7_bg_Destroy(bg);
  p7_hmm_Destroy(hmm);
  p7_hmmfile_Close(hfp);
  esl_alphabet_Destroy(abc);
  esl_stopwatch_Destroy(w);
  esl_randomness_Destroy(r);
  esl_getopts_Destroy(go);
  return 0;
}
Ejemplo n.º 14
0
int 
main(int argc, char **argv)
{
  ESL_GETOPTS    *go      = esl_getopts_CreateDefaultApp(options, 1, argc, argv, banner, usage);
  char           *hmmfile = esl_opt_GetArg(go, 1);
  ESL_STOPWATCH  *w       = esl_stopwatch_Create();
  ESL_RANDOMNESS *r       = esl_randomness_CreateFast(esl_opt_GetInteger(go, "-s"));
  ESL_ALPHABET   *abc     = NULL;
  P7_HMMFILE     *hfp     = NULL;
  P7_HMM         *hmm     = NULL;
  P7_BG          *bg      = NULL;
  P7_PROFILE     *gm      = NULL;
  P7_OPROFILE    *om      = NULL;
  P7_GMX         *gx      = NULL;
  P7_OMX         *fwd     = NULL;
  P7_TRACE       *tr      = NULL;
  int             L       = esl_opt_GetInteger(go, "-L");
  int             N       = esl_opt_GetInteger(go, "-N");
  ESL_DSQ        *dsq     = malloc(sizeof(ESL_DSQ) * (L+2));
  int             i;
  float           sc, fsc, vsc;
  float           bestsc  = -eslINFINITY;
  
  if (p7_hmmfile_Open(hmmfile, NULL, &hfp) != eslOK) p7_Fail("Failed to open HMM file %s", hmmfile);
  if (p7_hmmfile_Read(hfp, &abc, &hmm)     != eslOK) p7_Fail("Failed to read HMM");

  bg = p7_bg_Create(abc);                p7_bg_SetLength(bg, L);
  gm = p7_profile_Create(hmm->M, abc);   p7_ProfileConfig(hmm, bg, gm, L, p7_UNILOCAL);
  om = p7_oprofile_Create(gm->M, abc);   p7_oprofile_Convert(gm, om);

  fwd = p7_omx_Create(gm->M, L, L);
  gx  = p7_gmx_Create(gm->M, L);
  tr  = p7_trace_Create();
  esl_rsq_xfIID(r, bg->f, abc->K, L, dsq);

  p7_GViterbi(dsq, L, gm, gx,  &vsc);
  p7_Forward (dsq, L, om, fwd, &fsc);

  esl_stopwatch_Start(w);
  for (i = 0; i < N; i++)
    {
      p7_StochasticTrace(r, dsq, L, om, fwd, tr);
      p7_trace_Score(tr, dsq, gm, &sc);
      bestsc = ESL_MAX(bestsc, sc);
      p7_trace_Reuse(tr);
    }
  esl_stopwatch_Stop(w);
  esl_stopwatch_Display(stdout, w, "# CPU time: ");

  printf("forward sc   = %.4f nats\n", fsc);
  printf("viterbi sc   = %.4f nats\n", vsc);
  printf("max trace sc = %.4f nats\n", bestsc);

  free(dsq);
  p7_trace_Destroy(tr);
  p7_gmx_Destroy(gx);
  p7_omx_Destroy(fwd);
  p7_oprofile_Destroy(om);
  p7_profile_Destroy(gm);
  p7_bg_Destroy(bg);
  p7_hmm_Destroy(hmm);
  p7_hmmfile_Close(hfp);
  esl_alphabet_Destroy(abc);
  esl_stopwatch_Destroy(w);
  esl_randomness_Destroy(r);
  esl_getopts_Destroy(go);
  return 0;
}
Ejemplo n.º 15
0
int 
main(int argc, char **argv)
{
  ESL_GETOPTS    *go      = p7_CreateDefaultApp(options, 1, argc, argv, banner, usage);
  char           *hmmfile = esl_opt_GetArg(go, 1);
  ESL_STOPWATCH  *w       = esl_stopwatch_Create();
  ESL_RANDOMNESS *r       = esl_randomness_CreateFast(esl_opt_GetInteger(go, "-s"));
  ESL_ALPHABET   *abc     = NULL;
  P7_HMMFILE     *hfp     = NULL;
  P7_HMM         *hmm     = NULL;
  P7_BG          *bg      = NULL;
  P7_PROFILE     *gm      = NULL;
  P7_OPROFILE    *om      = NULL;
  P7_OMX         *ox1     = NULL;
  P7_OMX         *ox2     = NULL;
  int             L       = esl_opt_GetInteger(go, "-L");
  int             N       = esl_opt_GetInteger(go, "-N");
  ESL_DSQ        *dsq     = malloc(sizeof(ESL_DSQ) * (L+2));
  float           null2[p7_MAXCODE];
  int             i,j,d,pos;
  int             nsamples = 200;
  float           fsc, bsc;
  double          Mcs;

  if (p7_hmmfile_OpenE(hmmfile, NULL, &hfp, NULL) != eslOK) p7_Fail("Failed to open HMM file %s", hmmfile);
  if (p7_hmmfile_Read(hfp, &abc, &hmm)            != eslOK) p7_Fail("Failed to read HMM");

  bg = p7_bg_Create(abc);                 p7_bg_SetLength(bg, L);
  gm = p7_profile_Create(hmm->M, abc);    p7_ProfileConfig(hmm, bg, gm, L, p7_LOCAL);
  om = p7_oprofile_Create(gm->M, abc);    p7_oprofile_Convert(gm, om);
  p7_oprofile_ReconfigLength(om, L);

  ox1 = p7_omx_Create(gm->M, L, L);
  ox2 = p7_omx_Create(gm->M, L, L);

  esl_rsq_xfIID(r, bg->f, abc->K, L, dsq);
  p7_Forward (dsq, L, om, ox1,      &fsc);

  if (esl_opt_GetBoolean(go, "-t"))
    {
      P7_TRACE *tr   = p7_trace_Create();
      float    *n2sc = malloc(sizeof(float) * (L+1));

      esl_stopwatch_Start(w);
      for (i = 0; i < N; i++)
	{ /* This is approximately what p7_domaindef.c::region_trace_ensemble() is doing: */
	  for (j = 0; j < nsamples; j++)
	    {
	      p7_StochasticTrace(r, dsq, L, om, ox1, tr);
	      p7_trace_Index(tr);
	      pos = 1; 
	      for (d = 0; d < tr->ndom; d++)
		{
		  p7_Null2_ByTrace(om, tr, tr->tfrom[d], tr->tto[d], ox2, null2);
		  for (; pos <= tr->sqfrom[d]; pos++) n2sc[pos] += 1.0;
		  for (; pos < tr->sqto[d];    pos++) n2sc[pos] += null2[dsq[pos]];
		}
	      for (; pos <= L; pos++)  n2sc[pos] += 1.0;
	      p7_trace_Reuse(tr);
	    }

	  for (pos = 1; pos <= L; pos++)
	    n2sc[pos] = logf(n2sc[pos] / nsamples);
	}
      esl_stopwatch_Stop(w);

      free(n2sc);
      p7_trace_Destroy(tr);
    }
  else
    {
      p7_Backward(dsq, L, om, ox1, ox2, &bsc);
      p7_Decoding(om, ox1, ox2, ox2);              

      esl_stopwatch_Start(w);
      for (i = 0; i < N; i++)
	p7_Null2_ByExpectation(om, ox2, null2);
      esl_stopwatch_Stop(w);
    }


  Mcs = (double) N * (double) L * (double) gm->M * 1e-6 / (double) w->user;
  esl_stopwatch_Display(stdout, w, "# CPU time: ");
  printf("# M    = %d\n",   gm->M);
  printf("# %.1f Mc/s\n", Mcs);

  free(dsq);
  p7_omx_Destroy(ox1);
  p7_omx_Destroy(ox2);
  p7_oprofile_Destroy(om);
  p7_profile_Destroy(gm);
  p7_bg_Destroy(bg);
  p7_hmm_Destroy(hmm);
  p7_hmmfile_Close(hfp);
  esl_alphabet_Destroy(abc);
  esl_stopwatch_Destroy(w);
  esl_randomness_Destroy(r);
  esl_getopts_Destroy(go);
  return 0;
}
Ejemplo n.º 16
0
int 
main(int argc, char **argv)
{
  ESL_GETOPTS    *go      = p7_CreateDefaultApp(options, 2, argc, argv, banner, usage);
  char           *hmmfile = esl_opt_GetArg(go, 1);
  char           *seqfile = esl_opt_GetArg(go, 2);
  ESL_ALPHABET   *abc     = NULL;
  P7_HMMFILE     *hfp     = NULL;
  P7_HMM         *hmm     = NULL;
  P7_BG          *bg      = NULL;
  P7_PROFILE     *gm      = NULL;
  P7_OPROFILE    *om      = NULL;
  P7_OMX         *ox1     = NULL;
  P7_OMX         *ox2     = NULL;
  P7_GMX         *gx      = NULL;
  ESL_SQ         *sq      = NULL;
  ESL_SQFILE     *sqfp    = NULL;
  P7_TRACE       *tr      = NULL;
  int             format  = eslSQFILE_UNKNOWN;
  char            errbuf[eslERRBUFSIZE];
  float           fsc, bsc;
  float           accscore;
  int             status;

  /* Read in one HMM */
  if (p7_hmmfile_OpenE(hmmfile, NULL, &hfp, NULL) != eslOK) p7_Fail("Failed to open HMM file %s", hmmfile);
  if (p7_hmmfile_Read(hfp, &abc, &hmm)            != eslOK) p7_Fail("Failed to read HMM");
  p7_hmmfile_Close(hfp);
 
  /* Read in one sequence */
  sq     = esl_sq_CreateDigital(abc);
  status = esl_sqfile_OpenDigital(abc, seqfile, format, NULL, &sqfp);
  if      (status == eslENOTFOUND) p7_Fail("No such file.");
  else if (status == eslEFORMAT)   p7_Fail("Format unrecognized.");
  else if (status == eslEINVAL)    p7_Fail("Can't autodetect stdin or .gz.");
  else if (status != eslOK)        p7_Fail("Open failed, code %d.", status);
  if  (esl_sqio_Read(sqfp, sq) != eslOK) p7_Fail("Failed to read sequence");
  esl_sqfile_Close(sqfp);
 
  /* Configure a profile from the HMM */
  bg = p7_bg_Create(abc);                 p7_bg_SetLength(bg, sq->n);
  gm = p7_profile_Create(hmm->M, abc);    p7_ProfileConfig(hmm, bg, gm, sq->n, p7_LOCAL); /* multihit local: H3 default */
  om = p7_oprofile_Create(gm->M, abc);    p7_oprofile_Convert(gm, om);

  /* Allocations */
  ox1 = p7_omx_Create(gm->M, sq->n, sq->n);
  ox2 = p7_omx_Create(gm->M, sq->n, sq->n);
  gx  = p7_gmx_Create(gm->M, sq->n);
  tr  = p7_trace_CreateWithPP();
  p7_FLogsumInit();

  /* Run Forward, Backward; do OA fill and trace */
  p7_Forward (sq->dsq, sq->n, om, ox1,      &fsc);
  p7_Backward(sq->dsq, sq->n, om, ox1, ox2, &bsc);
  p7_Decoding(om, ox1, ox2, ox2);                   /* <gx2> is now the posterior decoding matrix */
  p7_OptimalAccuracy(om, ox2, ox1, &accscore);	    /* <gx1> is now the OA matrix */
  p7_OATrace(om, ox2, ox1, tr);
  
  if (esl_opt_GetBoolean(go, "-d")) { p7_omx_FDeconvert(ox2, gx);  p7_gmx_Dump(stdout, gx, p7_DEFAULT); }
  if (esl_opt_GetBoolean(go, "-m")) { p7_omx_FDeconvert(ox1, gx);  p7_gmx_Dump(stdout, gx, p7_DEFAULT); }

  p7_trace_Dump(stdout, tr, gm, sq->dsq);

  if (p7_trace_Validate(tr, abc, sq->dsq, errbuf) != eslOK) p7_Die("trace fails validation:\n%s\n", errbuf);

  printf("fwd = %.4f nats\n", fsc);
  printf("bck = %.4f nats\n", bsc);
  printf("acc = %.4f (%.2f%%)\n", accscore, accscore * 100. / (float) sq->n);

  /* Cleanup */
  esl_sq_Destroy(sq);
  p7_trace_Destroy(tr);
  p7_omx_Destroy(ox1);
  p7_omx_Destroy(ox2);
  p7_gmx_Destroy(gx);
  p7_oprofile_Destroy(om);
  p7_profile_Destroy(gm);
  p7_bg_Destroy(bg);
  p7_hmm_Destroy(hmm);
  esl_alphabet_Destroy(abc);
  esl_getopts_Destroy(go);
  return 0;
}
Ejemplo n.º 17
0
int 
main(int argc, char **argv)
{
  ESL_GETOPTS    *go      = esl_getopts_CreateDefaultApp(options, 2, argc, argv, banner, usage);
  char           *hmmfile = esl_opt_GetArg(go, 1);
  char           *seqfile = esl_opt_GetArg(go, 2);
  ESL_ALPHABET   *abc     = NULL;
  ESL_RANDOMNESS *rng     = esl_randomness_CreateFast(0);
  P7_HMMFILE     *hfp     = NULL;
  P7_HMM         *hmm     = NULL;
  P7_BG          *bg      = NULL;
  P7_PROFILE     *gm      = NULL;
  P7_OPROFILE    *om      = NULL;
  P7_GMX         *gx      = NULL;
  P7_OMX         *fwd     = NULL;
  P7_TRACE       *tr      = NULL;
  ESL_SQ         *sq      = NULL;
  ESL_SQFILE     *sqfp    = NULL;
  int             format  = eslSQFILE_UNKNOWN;
  int             N       = esl_opt_GetInteger(go, "-N");
  int             i;
  float           vsc, fsc, tsc;
  char            errbuf[eslERRBUFSIZE];
  int             status;

  /* Read in one HMM */
  if (p7_hmmfile_Open(hmmfile, NULL, &hfp) != eslOK) p7_Fail("Failed to open HMM file %s", hmmfile);
  if (p7_hmmfile_Read(hfp, &abc, &hmm)     != eslOK) p7_Fail("Failed to read HMM");

  /* Read in one sequence */
  sq     = esl_sq_CreateDigital(abc);
  status = esl_sqfile_Open(seqfile, format, NULL, &sqfp);
  if      (status == eslENOTFOUND) p7_Fail("No such file.");
  else if (status == eslEFORMAT)   p7_Fail("Format unrecognized.");
  else if (status == eslEINVAL)    p7_Fail("Can't autodetect stdin or .gz.");
  else if (status != eslOK)        p7_Fail("Open failed, code %d.", status);
  if  (esl_sqio_Read(sqfp, sq) != eslOK) p7_Fail("Failed to read sequence");

  /* create default null model, then create and optimize profile */
  bg = p7_bg_Create(abc);                p7_bg_SetLength(bg, sq->n);
  gm = p7_profile_Create(hmm->M, abc);   p7_ProfileConfig(hmm, bg, gm, sq->n, p7_LOCAL);
  om = p7_oprofile_Create(gm->M, abc);   p7_oprofile_Convert(gm, om);

  if (esl_opt_GetBoolean(go, "-p")) p7_oprofile_Dump(stdout, om);  

  fwd = p7_omx_Create(gm->M, sq->n, sq->n);
  gx  = p7_gmx_Create(gm->M, sq->n);
  tr  = p7_trace_Create();

  if (esl_opt_GetBoolean(go, "-m") == TRUE) p7_omx_SetDumpMode(stdout, fwd, TRUE); 
  p7_GViterbi(sq->dsq, sq->n, gm, gx,  &vsc);
  p7_Forward (sq->dsq, sq->n, om, fwd, &fsc);

  for (i = 0; i < N; i++)
    {
      p7_StochasticTrace(rng, sq->dsq, sq->n, om, fwd, tr);
      p7_trace_Score(tr, sq->dsq, gm, &tsc);
  
      if (esl_opt_GetBoolean(go, "-t") == TRUE) p7_trace_Dump(stdout, tr, gm, sq->dsq);
      if (p7_trace_Validate(tr, abc, sq->dsq, errbuf) != eslOK)  p7_Die("trace %d fails validation:\n%s\n", i, errbuf);

      printf("Sampled trace:  %.4f nats\n", tsc);
      p7_trace_Reuse(tr);
    }
  printf("Forward score:  %.4f nats\n", fsc);
  printf("Viterbi score:  %.4f nats\n", vsc);

  /* cleanup */
  esl_sq_Destroy(sq);
  esl_sqfile_Close(sqfp);
  p7_trace_Destroy(tr);
  p7_omx_Destroy(fwd);
  p7_gmx_Destroy(gx);
  p7_oprofile_Destroy(om);
  p7_profile_Destroy(gm);
  p7_bg_Destroy(bg);
  p7_hmm_Destroy(hmm);
  p7_hmmfile_Close(hfp);
  esl_randomness_Destroy(rng);
  esl_alphabet_Destroy(abc);
  esl_getopts_Destroy(go);
  return 0;
}
Ejemplo n.º 18
0
int 
main(int argc, char **argv)
{
  char           *hmmfile = argv[1];
  char           *seqfile = argv[2];
  ESL_ALPHABET   *abc     = NULL;
  P7_HMMFILE     *hfp     = NULL;
  P7_HMM         *hmm     = NULL;
  P7_BG          *bg      = NULL;
  P7_PROFILE     *gm      = NULL;
  P7_OPROFILE    *om      = NULL;
  P7_OMX         *ox      = NULL;
  P7_GMX         *gx      = NULL;
  ESL_SQ         *sq      = NULL;
  ESL_SQFILE     *sqfp    = NULL;
  int             format  = eslSQFILE_UNKNOWN;
  float           sc;
  int             status;

  /* Read in one HMM */
  if (p7_hmmfile_Open(hmmfile, NULL, &hfp) != eslOK) p7_Fail("Failed to open HMM file %s", hmmfile);
  if (p7_hmmfile_Read(hfp, &abc, &hmm)     != eslOK) p7_Fail("Failed to read HMM");

  /* Read in one sequence */
  sq     = esl_sq_CreateDigital(abc);
  status = esl_sqfile_Open(seqfile, format, NULL, &sqfp);
  if      (status == eslENOTFOUND) p7_Fail("No such file.");
  else if (status == eslEFORMAT)   p7_Fail("Format unrecognized.");
  else if (status == eslEINVAL)    p7_Fail("Can't autodetect stdin or .gz.");
  else if (status != eslOK)        p7_Fail("Open failed, code %d.", status);
  if  (esl_sqio_Read(sqfp, sq) != eslOK) p7_Fail("Failed to read sequence");

  /* create default null model, then create and optimize profile */
  bg = p7_bg_Create(abc);
  p7_bg_SetLength(bg, sq->n);
  gm = p7_profile_Create(hmm->M, abc);
  p7_ProfileConfig(hmm, bg, gm, sq->n, p7_LOCAL);
  om = p7_oprofile_Create(gm->M, abc);
  p7_oprofile_Convert(gm, om);
  p7_oprofile_Logify(om);

  /* allocate DP matrices, both a generic and an optimized one */
  ox = p7_omx_Create(gm->M, 0, sq->n);
  gx = p7_gmx_Create(gm->M, sq->n);

  /* Useful to place and compile in for debugging: 
     p7_oprofile_Dump(stdout, om);      dumps the optimized profile
     p7_omx_SetDumpMode(ox, TRUE);      makes the fast DP algorithms dump their matrices
     p7_gmx_Dump(stdout, gx);           dumps a generic DP matrix
  */

  p7_ViterbiScore(sq->dsq, sq->n, om, ox, &sc);  printf("viterbi (non-optimized):  %.2f nats\n", sc);
  p7_GViterbi    (sq->dsq, sq->n, gm, gx, &sc);  printf("viterbi (generic):        %.2f nats\n", sc);

  /* now in a real app, you'd need to convert raw nat scores to final bit
   * scores, by subtracting the null model score and rescaling.
   */

  /* cleanup */
  esl_sq_Destroy(sq);
  esl_sqfile_Close(sqfp);
  p7_omx_Destroy(ox);
  p7_gmx_Destroy(gx);
  p7_oprofile_Destroy(om);
  p7_profile_Destroy(gm);
  p7_bg_Destroy(bg);
  p7_hmm_Destroy(hmm);
  p7_hmmfile_Close(hfp);
  esl_alphabet_Destroy(abc);
  return 0;
}
Ejemplo n.º 19
0
int 
main(int argc, char **argv)
{
  ESL_GETOPTS    *go      = esl_getopts_CreateDefaultApp(options, 1, argc, argv, banner, usage);
  char           *hmmfile = esl_opt_GetArg(go, 1);
  ESL_STOPWATCH  *w       = esl_stopwatch_Create();
  ESL_RANDOMNESS *r       = esl_randomness_CreateFast(esl_opt_GetInteger(go, "-s"));
  ESL_ALPHABET   *abc     = NULL;
  P7_HMMFILE     *hfp     = NULL;
  P7_HMM         *hmm     = NULL;
  P7_BG          *bg      = NULL;
  P7_PROFILE     *gm      = NULL;
  P7_OPROFILE    *om      = NULL;
  P7_GMX         *gx      = NULL;
  P7_OMX         *fwd     = NULL;
  P7_OMX         *bck     = NULL;
  int             L       = esl_opt_GetInteger(go, "-L");
  int             N       = esl_opt_GetInteger(go, "-N");
  ESL_DSQ        *dsq     = malloc(sizeof(ESL_DSQ) * (L+2));
  int             i;
  float           fsc, bsc;
  float           fsc2, bsc2;
  double          base_time, bench_time, Mcs;

  p7_FLogsumInit();

  if (p7_hmmfile_Open(hmmfile, NULL, &hfp) != eslOK) p7_Fail("Failed to open HMM file %s", hmmfile);
  if (p7_hmmfile_Read(hfp, &abc, &hmm)     != eslOK) p7_Fail("Failed to read HMM");

  bg = p7_bg_Create(abc);
  p7_bg_SetLength(bg, L);
  gm = p7_profile_Create(hmm->M, abc);
  p7_ProfileConfig(hmm, bg, gm, L, p7_LOCAL);
  om = p7_oprofile_Create(gm->M, abc);
  p7_oprofile_Convert(gm, om);
  p7_oprofile_ReconfigLength(om, L);

  if (esl_opt_GetBoolean(go, "-x") && p7_FLogsumError(-0.4, -0.5) > 0.0001)
    p7_Fail("-x here requires p7_Logsum() recompiled in slow exact mode");

  if (esl_opt_GetBoolean(go, "-P")) {
    fwd = p7_omx_Create(gm->M, 0, L);
    bck = p7_omx_Create(gm->M, 0, L);
  } else {
    fwd = p7_omx_Create(gm->M, L, L);
    bck = p7_omx_Create(gm->M, L, L);
  }
  gx  = p7_gmx_Create(gm->M, L);

  /* Get a baseline time: how long it takes just to generate the sequences */
  esl_stopwatch_Start(w);
  for (i = 0; i < N; i++) esl_rsq_xfIID(r, bg->f, abc->K, L, dsq);
  esl_stopwatch_Stop(w);
  base_time = w->user;

  esl_stopwatch_Start(w);
  for (i = 0; i < N; i++)
    {
      esl_rsq_xfIID(r, bg->f, abc->K, L, dsq);
      if (esl_opt_GetBoolean(go, "-P")) {
	if (! esl_opt_GetBoolean(go, "-B"))  p7_ForwardParser (dsq, L, om,      fwd, &fsc);
	if (! esl_opt_GetBoolean(go, "-F"))  p7_BackwardParser(dsq, L, om, fwd, bck, &bsc);
      } else {
	if (! esl_opt_GetBoolean(go, "-B"))  p7_Forward (dsq, L, om,      fwd, &fsc);
	if (! esl_opt_GetBoolean(go, "-F"))  p7_Backward(dsq, L, om, fwd, bck, &bsc);
      }

      if (esl_opt_GetBoolean(go, "-c") || esl_opt_GetBoolean(go, "-x"))
	{
	  p7_GForward (dsq, L, gm, gx, &fsc2); 
	  p7_GBackward(dsq, L, gm, gx, &bsc2); 
	  printf("%.4f %.4f %.4f %.4f\n", fsc, bsc, fsc2, bsc2);  
	}
    }
  esl_stopwatch_Stop(w);
  bench_time = w->user - base_time;
  Mcs        = (double) N * (double) L * (double) gm->M * 1e-6 / (double) bench_time;
  esl_stopwatch_Display(stdout, w, "# CPU time: ");
  printf("# M    = %d\n",   gm->M);
  printf("# %.1f Mc/s\n", Mcs);

  free(dsq);
  p7_omx_Destroy(bck);
  p7_omx_Destroy(fwd);
  p7_gmx_Destroy(gx);
  p7_oprofile_Destroy(om);
  p7_profile_Destroy(gm);
  p7_bg_Destroy(bg);
  p7_hmm_Destroy(hmm);
  p7_hmmfile_Close(hfp);
  esl_alphabet_Destroy(abc);
  esl_stopwatch_Destroy(w);
  esl_randomness_Destroy(r);
  esl_getopts_Destroy(go);
  return 0;
}
Ejemplo n.º 20
0
int 
main(int argc, char **argv)
{
  ESL_GETOPTS    *go      = esl_getopts_CreateDefaultApp(options, 2, argc, argv, banner, usage);
  char           *hmmfile = esl_opt_GetArg(go, 1);
  char           *seqfile = esl_opt_GetArg(go, 2);
  ESL_ALPHABET   *abc     = NULL;
  P7_HMMFILE     *hfp     = NULL;
  P7_HMM         *hmm     = NULL;
  P7_BG          *bg      = NULL;
  P7_PROFILE     *gm      = NULL;
  P7_OPROFILE    *om      = NULL;
  P7_GMX         *gx      = NULL;
  P7_OMX         *fwd     = NULL;
  P7_OMX         *bck     = NULL;
  ESL_SQ         *sq      = NULL;
  ESL_SQFILE     *sqfp    = NULL;
  int             format  = eslSQFILE_UNKNOWN;
  float           fraw, braw, nullsc, fsc;
  float           gfraw, gbraw, gfsc;
  double          P, gP;
  int             status;

  /* Read in one HMM */
  if (p7_hmmfile_Open(hmmfile, NULL, &hfp) != eslOK) p7_Fail("Failed to open HMM file %s", hmmfile);
  if (p7_hmmfile_Read(hfp, &abc, &hmm)     != eslOK) p7_Fail("Failed to read HMM");

  /* Open sequence file for reading */
  sq     = esl_sq_CreateDigital(abc);
  status = esl_sqfile_Open(seqfile, format, NULL, &sqfp);
  if      (status == eslENOTFOUND) p7_Fail("No such file.");
  else if (status == eslEFORMAT)   p7_Fail("Format unrecognized.");
  else if (status == eslEINVAL)    p7_Fail("Can't autodetect stdin or .gz.");
  else if (status != eslOK)        p7_Fail("Open failed, code %d.", status);

  /* create default null model, then create and optimize profile */
  bg = p7_bg_Create(abc);               
  p7_bg_SetLength(bg, sq->n);
  gm = p7_profile_Create(hmm->M, abc); 
  p7_ProfileConfig(hmm, bg, gm, sq->n, p7_UNILOCAL);
  om = p7_oprofile_Create(gm->M, abc);
  p7_oprofile_Convert(gm, om);

  /* p7_oprofile_Dump(stdout, om);  */

  /* allocate DP matrices for O(M+L) parsers */
  fwd = p7_omx_Create(gm->M, 0, sq->n);
  bck = p7_omx_Create(gm->M, 0, sq->n);
  gx  = p7_gmx_Create(gm->M,    sq->n);

  /* allocate DP matrices for O(ML) fills */
  /* fwd = p7_omx_Create(gm->M, sq->n, sq->n); */
  /* bck = p7_omx_Create(gm->M, sq->n, sq->n); */

  /* p7_omx_SetDumpMode(stdout, fwd, TRUE); */     /* makes the fast DP algorithms dump their matrices */
  /* p7_omx_SetDumpMode(stdout, bck, TRUE); */  

  while ((status = esl_sqio_Read(sqfp, sq)) == eslOK)
    {
      p7_oprofile_ReconfigLength(om, sq->n);
      p7_ReconfigLength(gm,          sq->n);
      p7_bg_SetLength(bg,            sq->n);
      p7_omx_GrowTo(fwd, om->M, 0,   sq->n); 
      p7_omx_GrowTo(bck, om->M, 0,   sq->n); 
      p7_gmx_GrowTo(gx,  gm->M,      sq->n); 

      p7_bg_NullOne  (bg, sq->dsq, sq->n, &nullsc);
    
      p7_ForwardParser (sq->dsq, sq->n, om,      fwd, &fraw);
      p7_BackwardParser(sq->dsq, sq->n, om, fwd, bck, &braw);

      /* p7_Forward (sq->dsq, sq->n, om,      fwd, &fsc);        printf("forward:              %.2f nats\n", fsc);  */
      /* p7_Backward(sq->dsq, sq->n, om, fwd, bck, &bsc);        printf("backward:             %.2f nats\n", bsc);  */

      /* Comparison to other F/B implementations */
      p7_GForward     (sq->dsq, sq->n, gm, gx,  &gfraw);
      p7_GBackward    (sq->dsq, sq->n, gm, gx,  &gbraw);

      /* p7_gmx_Dump(stdout, gx);  */

      fsc  =  (fraw-nullsc) / eslCONST_LOG2;
      gfsc = (gfraw-nullsc) / eslCONST_LOG2;
      P  = esl_exp_surv(fsc,   om->evparam[p7_FTAU],  om->evparam[p7_FLAMBDA]);
      gP = esl_exp_surv(gfsc,  gm->evparam[p7_FTAU],  gm->evparam[p7_FLAMBDA]);

      if (esl_opt_GetBoolean(go, "-1"))
	{
	  printf("%-30s\t%-20s\t%9.2g\t%6.1f\t%9.2g\t%6.1f\n", sq->name, hmm->name, P, fsc, gP, gfsc);
	}
      else if (esl_opt_GetBoolean(go, "-P"))
	{ /* output suitable for direct use in profmark benchmark postprocessors: */
	  printf("%g\t%.2f\t%s\t%s\n", P, fsc, sq->name, hmm->name);
	}
      else
	{
	  printf("target sequence:      %s\n",        sq->name);
	  printf("fwd filter raw score: %.2f nats\n", fraw);
	  printf("bck filter raw score: %.2f nats\n", braw);
	  printf("null score:           %.2f nats\n", nullsc);
	  printf("per-seq score:        %.2f bits\n", fsc);
	  printf("P-value:              %g\n",        P);
	  printf("GForward raw score:   %.2f nats\n", gfraw);
	  printf("GBackward raw score:  %.2f nats\n", gbraw);
	  printf("GForward seq score:   %.2f bits\n", gfsc);
	  printf("GForward P-value:     %g\n",        gP);
	}

      esl_sq_Reuse(sq);
    }

  /* cleanup */
  esl_sq_Destroy(sq);
  esl_sqfile_Close(sqfp);
  p7_omx_Destroy(bck);
  p7_omx_Destroy(fwd);
  p7_gmx_Destroy(gx);
  p7_oprofile_Destroy(om);
  p7_profile_Destroy(gm);
  p7_bg_Destroy(bg);
  p7_hmm_Destroy(hmm);
  p7_hmmfile_Close(hfp);
  esl_alphabet_Destroy(abc);
  esl_getopts_Destroy(go);
  return 0;
}
Ejemplo n.º 21
0
int 
main(int argc, char **argv)
{
  ESL_GETOPTS    *go      = esl_getopts_CreateDefaultApp(options, 1, argc, argv, banner, usage);
  char           *hmmfile = esl_opt_GetArg(go, 1);
  ESL_STOPWATCH  *w       = esl_stopwatch_Create();
  ESL_RANDOMNESS *r       = esl_randomness_CreateFast(esl_opt_GetInteger(go, "-s"));
  ESL_ALPHABET   *abc     = NULL;
  P7_HMMFILE     *hfp     = NULL;
  P7_HMM         *hmm     = NULL;
  P7_BG          *bg      = NULL;
  P7_PROFILE     *gm      = NULL;
  P7_OPROFILE    *om      = NULL;
  P7_OMX         *fwd     = NULL;
  P7_OMX         *bck     = NULL;
  P7_OMX         *pp      = NULL;
  int             L       = esl_opt_GetInteger(go, "-L");
  int             N       = esl_opt_GetInteger(go, "-N");
  ESL_DSQ        *dsq     = malloc(sizeof(ESL_DSQ) * (L+2));
  int             i;
  float           fsc, bsc;
  double          Mcs;

  if (p7_hmmfile_Open(hmmfile, NULL, &hfp) != eslOK) p7_Fail("Failed to open HMM file %s", hmmfile);
  if (p7_hmmfile_Read(hfp, &abc, &hmm)     != eslOK) p7_Fail("Failed to read HMM");

  bg = p7_bg_Create(abc);                 p7_bg_SetLength(bg, L);
  gm = p7_profile_Create(hmm->M, abc);    p7_ProfileConfig(hmm, bg, gm, L, p7_LOCAL);
  om = p7_oprofile_Create(gm->M, abc);    p7_oprofile_Convert(gm, om);
  p7_oprofile_ReconfigLength(om, L);

  fwd = p7_omx_Create(gm->M, L, L);
  bck = p7_omx_Create(gm->M, L, L);
  pp  = p7_omx_Create(gm->M, L, L);

  esl_rsq_xfIID(r, bg->f, abc->K, L, dsq);
  p7_Forward (dsq, L, om, fwd,      &fsc);
  p7_Backward(dsq, L, om, fwd, bck, &bsc);

  esl_stopwatch_Start(w);
  for (i = 0; i < N; i++)
    p7_Decoding(om, fwd, bck, pp);              
  esl_stopwatch_Stop(w);

  Mcs = (double) N * (double) L * (double) gm->M * 1e-6 / (double) w->user;
  esl_stopwatch_Display(stdout, w, "# CPU time: ");
  printf("# M    = %d\n",   gm->M);
  printf("# %.1f Mc/s\n", Mcs);

  free(dsq);
  p7_omx_Destroy(fwd);
  p7_omx_Destroy(bck);
  p7_omx_Destroy(pp);
  p7_oprofile_Destroy(om);
  p7_profile_Destroy(gm);
  p7_bg_Destroy(bg);
  p7_hmm_Destroy(hmm);
  p7_hmmfile_Close(hfp);
  esl_alphabet_Destroy(abc);
  esl_stopwatch_Destroy(w);
  esl_randomness_Destroy(r);
  esl_getopts_Destroy(go);
  return eslOK;
}
Ejemplo n.º 22
0
/* 
 * 1. Compare accscore to GOptimalAccuracy().
 * 2. Compare trace to GOATrace().
 * 
 * Note: This test is subject to some expected noise and can fail
 * for entirely innocent reasons. Generic Forward/Backward calculations with
 * p7_GForward(), p7_GBackward() use coarse-grain table lookups to sum
 * log probabilities, and sufficient roundoff error can accumulate to
 * change the optimal accuracy traceback, causing this test to fail.
 * So, if optacc_utest fails, before you go looking for bugs, first
 * go to ../logsum.c, change the #ifdef to activate the slow/accurate 
 * version, recompile and rerun optacc_utest. If the failure goes away,
 * you can ignore it.   - SRE, Wed Dec 17 09:45:31 2008
 */
static void
utest_optacc(ESL_GETOPTS *go, ESL_RANDOMNESS *r, ESL_ALPHABET *abc, P7_BG *bg, int M, int L, int N)
{
  char        *msg = "optimal accuracy unit test failed";
  P7_HMM      *hmm = NULL;
  P7_PROFILE  *gm  = NULL;
  P7_OPROFILE *om  = NULL;
  ESL_SQ      *sq  = esl_sq_CreateDigital(abc);
  P7_OMX      *ox1 = p7_omx_Create(M, L, L);
  P7_OMX      *ox2 = p7_omx_Create(M, L, L);
  P7_GMX      *gx1 = p7_gmx_Create(M, L);
  P7_GMX      *gx2 = p7_gmx_Create(M, L);
  P7_TRACE    *tr  = p7_trace_CreateWithPP();
  P7_TRACE    *trg = p7_trace_CreateWithPP();
  P7_TRACE    *tro = p7_trace_CreateWithPP();
  float        accscore_o;
  float        fsc, bsc, accscore;
  float        fsc_g, bsc_g, accscore_g, accscore_g2;
  float        pptol = 0.01;
  float        sctol = 0.001;
  float        gtol;

  p7_FLogsumInit();
  gtol = ( (p7_FLogsumError(-0.4, -0.5) > 0.0001) ?  0.1 : 0.001);

  if (p7_oprofile_Sample(r, abc, bg, M, L, &hmm, &gm, &om)!= eslOK) esl_fatal(msg);
  while (N--)
    {
      if (p7_ProfileEmit(r, hmm, gm, bg, sq, tro)         != eslOK) esl_fatal(msg);

      if (p7_omx_GrowTo(ox1, M, sq->n, sq->n)             != eslOK) esl_fatal(msg);
      if (p7_omx_GrowTo(ox2, M, sq->n, sq->n)             != eslOK) esl_fatal(msg);
      if (p7_gmx_GrowTo(gx1, M, sq->n)                    != eslOK) esl_fatal(msg);
      if (p7_gmx_GrowTo(gx2, M, sq->n)                    != eslOK) esl_fatal(msg);

      if (p7_Forward (sq->dsq, sq->n, om, ox1,      &fsc) != eslOK) esl_fatal(msg);
      if (p7_Backward(sq->dsq, sq->n, om, ox1, ox2, &bsc) != eslOK) esl_fatal(msg);
      if (p7_Decoding(om, ox1, ox2, ox2)                  != eslOK) esl_fatal(msg);
      if (p7_OptimalAccuracy(om, ox2, ox1, &accscore)     != eslOK) esl_fatal(msg);

#if 0
      p7_omx_FDeconvert(ox1, gx1); 
      p7_gmx_Dump(stdout, gx1, p7_DEFAULT); 
      p7_omx_FDeconvert(ox2, gx1); 
      p7_gmx_Dump(stdout, gx1, p7_DEFAULT); 
#endif
      if (p7_OATrace(om, ox2, ox1, tr)                    != eslOK) esl_fatal(msg);
      
      if (p7_GForward (sq->dsq, sq->n, gm, gx1, &fsc_g)   != eslOK) esl_fatal(msg);
      if (p7_GBackward(sq->dsq, sq->n, gm, gx2, &bsc_g)   != eslOK) esl_fatal(msg);

#if 0
      p7_gmx_Dump(stdout, gx1, p7_DEFAULT); /* fwd */
      p7_gmx_Dump(stdout, gx2, p7_DEFAULT); /* bck */
#endif

      if (p7_GDecoding(gm, gx1, gx2, gx2)                 != eslOK) esl_fatal(msg);
      if (p7_GOptimalAccuracy(gm, gx2, gx1, &accscore_g)  != eslOK) esl_fatal(msg);
      
#if 0
      p7_gmx_Dump(stdout, gx1, p7_DEFAULT); /* oa */
      p7_gmx_Dump(stdout, gx2, p7_DEFAULT); /* pp */
#endif
      if (p7_GOATrace(gm, gx2, gx1, trg)                  != eslOK) esl_fatal(msg);

      if (p7_trace_SetPP(tro, gx2)                        != eslOK) esl_fatal(msg);

      if (esl_opt_GetBoolean(go, "--traces"))
	{
	  p7_trace_Dump(stdout, tro, gm, sq->dsq);
	  p7_trace_Dump(stdout, tr,  gm, sq->dsq);
	  p7_trace_Dump(stdout, trg, gm, sq->dsq);
	}

      if (p7_trace_Validate(tr,  abc, sq->dsq, NULL)      != eslOK) esl_fatal(msg);
      if (p7_trace_Validate(trg, abc, sq->dsq, NULL)      != eslOK) esl_fatal(msg);
      if (p7_trace_Compare(tr, trg, pptol)                != eslOK) esl_fatal(msg);

      accscore_o  = p7_trace_GetExpectedAccuracy(tro); /* according to gx2; see p7_trace_SetPP() call above */
      accscore_g2 = p7_trace_GetExpectedAccuracy(trg);

#if 0
      printf("%f %f %f %f\n", accscore, accscore_g, accscore_g2, accscore_o);
#endif

      if (esl_FCompare(fsc,        bsc,         sctol)    != eslOK) esl_fatal(msg);
      if (esl_FCompare(fsc_g,      bsc_g,       gtol)     != eslOK) esl_fatal(msg);
      if (esl_FCompare(fsc,        fsc_g,       gtol)     != eslOK) esl_fatal(msg);
      if (esl_FCompare(accscore,   accscore_g,  gtol)     != eslOK) esl_fatal(msg);
      if (esl_FCompare(accscore_g, accscore_g2, gtol)     != eslOK) esl_fatal(msg);
      if (accscore_g2 < accscore_o)                                 esl_fatal(msg);
      /* the above deserves explanation:
       *  - accscore_o is the accuracy of the originally emitted trace, according
       *      to the generic posterior decoding matrix <gx2>. This is a lower bound
       *      on the expected # of accurately aligned residues found by a DP 
       *      optimization.
       *  - accscore is the accuracy found by the fast (vector) code DP implementation.
       *  - accscore_g is the accuracy found by the generic DP implementation.
       *      accscore and accscore_g should be nearly identical,
       *      within tolerance of roundoff error accumulation and
       *      the imprecision of Logsum() tables.
       *  - accscore_g2 is the accuracy of the traceback identified by the generic
       *      DP implementation. It should be identical (within order-of-evaluation
       *      roundoff error) to accscore_g.
       *      
       * the "accscore_g2 < accscore_o" test is carefully contrived.
       * accscore_o is a theoretical lower bound but because of fp error, 
       * accscore and (much more rarely) even accscore_g can exceed accscore_o.
       * accscore_g2, however, is calculated with identical order of evaluation
       * as accscore_o if the optimal trace does turn out to be identical to 
       * the originally emitted trace. It should be extremely unlikely (though
       * not impossible) for accscore_o to exceed accscore_g2. (The DP algorithm
       * would have to identify a trace that was different than the original trace,
       * which the DP algorithm, by order-of-evaluation, assigned higher accuracy,
       * but order-of-evaluation in traceback dependent code assigned lower accuracy.
       * [xref J5/29]
       */

      esl_sq_Reuse(sq);
      p7_trace_Reuse(tr);
      p7_trace_Reuse(trg);
      p7_trace_Reuse(tro);
    }

  p7_trace_Destroy(tro);
  p7_trace_Destroy(trg);
  p7_trace_Destroy(tr);
  p7_gmx_Destroy(gx2);
  p7_gmx_Destroy(gx1);
  p7_omx_Destroy(ox2);
  p7_omx_Destroy(ox1);  
  esl_sq_Destroy(sq);
  p7_oprofile_Destroy(om);
  p7_profile_Destroy(gm);
  p7_hmm_Destroy(hmm);
}